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#define _FILE_OFFSET_BITS 64 |
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#include <stdio.h> |
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#include <stdlib.h> |
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#include <string.h> |
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#include "params.h" |
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#include "tcProps.h" |
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#include "readWrite.h" |
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#include "scdCorr.h" |
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#include "directorHead.h" |
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#include "directorWhole.h" |
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#include "rmsd.h" |
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#include "gofz.h" |
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|
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#define VERSION_MAJOR 0 |
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#define VERSION_MINOR 1 |
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char *programName; /*the name of the program */ |
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void usage(void); |
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int main( int argC, char *argV[] ){ |
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// list of 'a priori' constants |
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const int nLipAtoms = NL_ATOMS; |
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const int nBonds = NBONDS; |
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const int nLipids = NLIPIDS; |
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const int nSSD = NSSD; |
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const int nAtoms = nLipAtoms * nLipids + nSSD; |
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|
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// different needed variables |
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|
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struct atomCoord atoms[nAtoms]; |
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int i,j,k; |
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char* outPrefix; // the output prefix |
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char currentFlag; // used in parsing the flags |
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int done = 0; // multipurpose boolean |
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int havePrefix; // boolean for the output prefix |
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mmeineke |
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int haveMaxLength; |
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char* conversionCheck; |
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int conversionError; |
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int optionError; |
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char* rmsdName; |
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char* pair1; |
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char* pair2; |
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int scdCorr; |
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double startTime; |
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double avgXY; |
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double maxLength; |
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|
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int directorHead, directorWhole, doRMSD, doGofz, doAvgXY; |
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enum atomNames rmsdType; |
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mmeineke |
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|
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// system initialization |
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|
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isScanned = 0; |
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fileOpen = 0; |
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nFrames = 0; |
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frameTimes = NULL; |
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|
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outPrefix = NULL; |
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inName = NULL; |
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haveMaxLength = 0; |
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conversionError = 0; |
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optionError = 0; |
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havePrefix = 0; |
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scdCorr = 0; |
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startTime = 0.0; |
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directorHead = 0; |
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directorWhole = 0; |
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doRMSD = 0; |
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doGofz = 0; |
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doAvgXY = 0; |
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|
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|
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// parse the command line |
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programName = argV[0]; /*save the program name in case we need it*/ |
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for( i = 1; i < argC; i++){ |
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if(argV[i][0] =='-'){ |
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// parse the option |
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if(argV[i][1] == '-' ){ |
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// parse long word options |
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if( !strcmp( argV[i], "--rmsd" ) ){ |
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|
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doRMSD = 1; |
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i++; |
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if( i>=argC ){ |
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fprintf( stderr, |
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"\n" |
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"not enough arguments for --rmsd\n"); |
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usage(); |
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exit(0); |
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} |
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rmsdName = argV[i]; |
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|
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if( !strcmp(rmsdName, "HEAD") ) rmsdType = HEAD; |
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else if( !strcmp(rmsdName, "CH") ) rmsdType = CH; |
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else if( !strcmp(rmsdName, "CH2") )rmsdType = CH2; |
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else if( !strcmp(rmsdName, "CH3") )rmsdType = CH3; |
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else if( !strcmp(rmsdName, "SSD") )rmsdType = SSD; |
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else if( !strcmp(rmsdName, "COM") )rmsdType = COM; |
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else{ |
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fprintf( stderr, |
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"Unrecognized rmsd atom type \"%s\"\n", |
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rmsdName ); |
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exit(0); |
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} |
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|
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} |
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else if( !strcmp( argV[i], "--gofrTheta" ) ){ |
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i++; |
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if( i>=argC ){ |
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fprintf( stderr, |
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"\n" |
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"not enough arguments for --gofrTheta\n"); |
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usage(); |
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exit(0); |
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} |
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pair1 = argV[i]; |
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i++; |
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if( i>=argC ){ |
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fprintf( stderr, |
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"\n" |
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"not enough arguments for --gofrTheta\n"); |
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usage(); |
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exit(0); |
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} |
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pair2 = argV[i]; |
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} |
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else if( !strcmp( argV[i], "--gofrOmega" ) ){ |
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i++; |
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if( i>=argC ){ |
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fprintf( stderr, |
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"\n" |
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"not enough arguments for --gofrOmega\n"); |
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usage(); |
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exit(0); |
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} |
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pair1 = argV[i]; |
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i++; |
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if( i>=argC ){ |
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fprintf( stderr, |
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"\n" |
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"not enough arguments for --gofrOmega\n"); |
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usage(); |
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exit(0); |
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} |
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pair2 = argV[i]; |
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} |
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else if( !strcmp( argV[i], "--version") ){ |
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printf("\n" |
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"tcProps version %d.%d\n" |
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"\n", |
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VERSION_MAJOR, VERSION_MINOR ); |
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exit(0); |
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} |
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else if( !strcmp( argV[i], "--help") ){ |
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usage(); |
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exit(0); |
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} |
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// anything else is an error |
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else{ |
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fprintf( stderr, |
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"Invalid option \"%s\"\n", argV[i] ); |
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usage(); |
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exit(0); |
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} |
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} |
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else{ |
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// parse single character options |
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done =0; |
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j = 1; |
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currentFlag = argV[i][j]; |
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while( (currentFlag != '\0') && (!done) ){ |
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switch(currentFlag){ |
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case 'o': |
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// -o <prefix> => the output prefix. |
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j++; |
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currentFlag = argV[i][j]; |
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if( currentFlag != '\0' ) optionError = 1; |
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216 |
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if( optionError ){ |
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fprintf( stderr, |
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"\n" |
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"The -o flag should end an option sequence.\n" |
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" example: -r <outname> *NOT* -or <outname>\n" ); |
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usage(); |
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exit(0); |
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} |
224 |
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i++; |
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if( i>=argC ){ |
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fprintf( stderr, |
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"\n" |
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"not enough arguments for -o\n"); |
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usage(); |
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exit(0); |
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} |
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outPrefix = argV[i]; |
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if( outPrefix[0] == '-' ) optionError = 1; |
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if( optionError ){ |
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fprintf( stderr, |
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"\n" |
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"\"%s\" is not a valid out prefix/name.\n" |
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"Out prefix/name should not begin with a dash.\n", |
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outPrefix ); |
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usage(); |
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exit(0); |
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} |
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havePrefix = 1; |
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done = 1; |
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break; |
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case 'l': |
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// -l <double> set <double> to the maxLength |
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mmeineke |
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haveMaxLength = 1; |
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mmeineke |
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j++; |
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currentFlag = argV[i][j]; |
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if( currentFlag != '\0' ) optionError = 1; |
259 |
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260 |
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if( optionError ){ |
261 |
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fprintf( stderr, |
262 |
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"\n" |
263 |
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"The -l flag should end an option sequence.\n" |
264 |
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" example: -sl <double> *NOT* -ls <double>\n" ); |
265 |
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usage(); |
266 |
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exit(0); |
267 |
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} |
268 |
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269 |
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i++; |
270 |
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if( i>=argC ){ |
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fprintf( stderr, |
272 |
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"\n" |
273 |
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"not enough arguments for -l\n"); |
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usage(); |
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exit(0); |
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} |
277 |
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278 |
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maxLength = atof( argV[i] ); |
279 |
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280 |
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done = 1; |
281 |
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282 |
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break; |
283 |
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284 |
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case 't': |
285 |
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// -t <double> set <double> to the startTime |
286 |
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287 |
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j++; |
288 |
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currentFlag = argV[i][j]; |
289 |
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290 |
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if( currentFlag != '\0' ) optionError = 1; |
291 |
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292 |
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if( optionError ){ |
293 |
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fprintf( stderr, |
294 |
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"\n" |
295 |
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"The -t flag should end an option sequence.\n" |
296 |
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" example: -st <double> *NOT* -ts <double>\n" ); |
297 |
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usage(); |
298 |
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exit(0); |
299 |
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} |
300 |
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301 |
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i++; |
302 |
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if( i>=argC ){ |
303 |
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fprintf( stderr, |
304 |
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"\n" |
305 |
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"not enough arguments for -t\n"); |
306 |
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usage(); |
307 |
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exit(0); |
308 |
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} |
309 |
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310 |
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startTime = atof( argV[i] ); |
311 |
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done = 1; |
312 |
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break; |
313 |
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314 |
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case 's': |
315 |
mmeineke |
1060 |
// -s turn on Scd corr |
316 |
mmeineke |
1058 |
|
317 |
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scdCorr = 1; |
318 |
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break; |
319 |
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320 |
mmeineke |
1060 |
case 'h': |
321 |
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// -h turn on director head |
322 |
mmeineke |
1058 |
|
323 |
mmeineke |
1060 |
directorHead = 1; |
324 |
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break; |
325 |
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326 |
mmeineke |
1062 |
case 'w': |
327 |
mmeineke |
1080 |
// -w turn on director head |
328 |
mmeineke |
1060 |
|
329 |
mmeineke |
1062 |
directorWhole = 1; |
330 |
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break; |
331 |
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332 |
mmeineke |
1080 |
case 'g': |
333 |
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// -g turn on gofZ |
334 |
mmeineke |
1062 |
|
335 |
mmeineke |
1080 |
doGofz = 1; |
336 |
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break; |
337 |
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338 |
mmeineke |
1085 |
case 'v': |
339 |
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// -v turn on average XY |
340 |
mmeineke |
1080 |
|
341 |
mmeineke |
1085 |
doAvgXY = 1; |
342 |
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break; |
343 |
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344 |
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345 |
mmeineke |
1058 |
default: |
346 |
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347 |
mmeineke |
1060 |
fprintf( stderr, |
348 |
mmeineke |
1058 |
"\n" |
349 |
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"Bad option \"-%c\"\n", currentFlag); |
350 |
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usage(); |
351 |
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exit(0); |
352 |
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} |
353 |
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j++; |
354 |
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currentFlag = argV[i][j]; |
355 |
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} |
356 |
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} |
357 |
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} |
358 |
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359 |
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else{ |
360 |
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361 |
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if( inName != NULL ){ |
362 |
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fprintf( stderr, |
363 |
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"Error at \"%s\", program does not currently support\n" |
364 |
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"more than one input dump file.\n" |
365 |
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"\n", |
366 |
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argV[i]); |
367 |
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usage(); |
368 |
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exit(0); |
369 |
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} |
370 |
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371 |
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inName = argV[i]; |
372 |
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373 |
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} |
374 |
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} |
375 |
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376 |
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if( inName == NULL ){ |
377 |
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fprintf( stderr, |
378 |
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"Error, dump file is needed to run.\n" ); |
379 |
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usage(); |
380 |
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exit(0); |
381 |
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} |
382 |
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|
383 |
mmeineke |
1060 |
if( outPrefix == NULL ) |
384 |
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outPrefix = inName; |
385 |
mmeineke |
1058 |
|
386 |
mmeineke |
1060 |
|
387 |
mmeineke |
1049 |
// initialize the arrays |
388 |
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|
389 |
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for(i=0;i<nLipids;i++){ |
390 |
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|
391 |
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atoms[nLipAtoms*i+0].type = HEAD; |
392 |
mmeineke |
1062 |
atoms[nLipAtoms*i+0].mass = 72; |
393 |
mmeineke |
1052 |
atoms[nLipAtoms*i+0].u[0] = 0.0; |
394 |
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atoms[nLipAtoms*i+0].u[1] = 0.0; |
395 |
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atoms[nLipAtoms*i+0].u[2] = 1.0; |
396 |
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|
397 |
mmeineke |
1062 |
|
398 |
mmeineke |
1049 |
|
399 |
|
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atoms[nLipAtoms*i+1].type = CH2; |
400 |
mmeineke |
1062 |
atoms[nLipAtoms*i+1].mass = 14.03; |
401 |
mmeineke |
1049 |
|
402 |
|
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atoms[nLipAtoms*i+2].type = CH; |
403 |
mmeineke |
1062 |
atoms[nLipAtoms*i+2].mass = 13.02; |
404 |
mmeineke |
1049 |
|
405 |
|
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atoms[nLipAtoms*i+3].type = CH2; |
406 |
mmeineke |
1062 |
atoms[nLipAtoms*i+3].mass = 14.03; |
407 |
mmeineke |
1049 |
|
408 |
|
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atoms[nLipAtoms*i+4].type = CH2; |
409 |
mmeineke |
1062 |
atoms[nLipAtoms*i+4].mass = 14.03; |
410 |
mmeineke |
1049 |
|
411 |
|
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atoms[nLipAtoms*i+5].type = CH2; |
412 |
mmeineke |
1062 |
atoms[nLipAtoms*i+5].mass = 14.03; |
413 |
mmeineke |
1049 |
|
414 |
|
|
atoms[nLipAtoms*i+6].type = CH2; |
415 |
mmeineke |
1062 |
atoms[nLipAtoms*i+6].mass = 14.03; |
416 |
mmeineke |
1049 |
|
417 |
|
|
atoms[nLipAtoms*i+7].type = CH2; |
418 |
mmeineke |
1062 |
atoms[nLipAtoms*i+7].mass = 14.03; |
419 |
mmeineke |
1049 |
|
420 |
|
|
atoms[nLipAtoms*i+8].type = CH2; |
421 |
mmeineke |
1062 |
atoms[nLipAtoms*i+8].mass = 14.03; |
422 |
mmeineke |
1049 |
|
423 |
|
|
atoms[nLipAtoms*i+9].type = CH2; |
424 |
mmeineke |
1062 |
atoms[nLipAtoms*i+9].mass = 14.03; |
425 |
mmeineke |
1049 |
|
426 |
|
|
atoms[nLipAtoms*i+10].type = CH3; |
427 |
mmeineke |
1062 |
atoms[nLipAtoms*i+10].mass = 15.04; |
428 |
mmeineke |
1049 |
|
429 |
|
|
atoms[nLipAtoms*i+11].type = CH2; |
430 |
mmeineke |
1062 |
atoms[nLipAtoms*i+11].mass = 14.03; |
431 |
mmeineke |
1049 |
|
432 |
|
|
atoms[nLipAtoms*i+12].type = CH2; |
433 |
mmeineke |
1062 |
atoms[nLipAtoms*i+12].mass = 14.03; |
434 |
mmeineke |
1049 |
|
435 |
mmeineke |
1062 |
atoms[nLipAtoms*i+13].type = CH2; |
436 |
|
|
atoms[nLipAtoms*i+13].mass = 14.03; |
437 |
mmeineke |
1049 |
|
438 |
|
|
atoms[nLipAtoms*i+14].type = CH2; |
439 |
mmeineke |
1062 |
atoms[nLipAtoms*i+14].mass = 14.03; |
440 |
mmeineke |
1049 |
|
441 |
|
|
atoms[nLipAtoms*i+15].type = CH2; |
442 |
mmeineke |
1062 |
atoms[nLipAtoms*i+15].mass = 14.03; |
443 |
mmeineke |
1049 |
|
444 |
|
|
atoms[nLipAtoms*i+16].type = CH2; |
445 |
mmeineke |
1062 |
atoms[nLipAtoms*i+16].mass = 14.03; |
446 |
mmeineke |
1049 |
|
447 |
|
|
atoms[nLipAtoms*i+17].type = CH2; |
448 |
mmeineke |
1062 |
atoms[nLipAtoms*i+17].mass = 14.03; |
449 |
mmeineke |
1049 |
|
450 |
|
|
atoms[nLipAtoms*i+18].type = CH3; |
451 |
mmeineke |
1062 |
atoms[nLipAtoms*i+18].mass = 15.04; |
452 |
mmeineke |
1049 |
} |
453 |
|
|
|
454 |
mmeineke |
1052 |
for(i=(nLipAtoms*nLipids);i<nAtoms;i++){ |
455 |
mmeineke |
1049 |
atoms[i].type = SSD; |
456 |
mmeineke |
1062 |
atoms[i].mass = 18.03; |
457 |
mmeineke |
1052 |
atoms[i].u[0] = 0.0; |
458 |
|
|
atoms[i].u[1] = 0.0; |
459 |
|
|
atoms[i].u[2] = 1.0; |
460 |
mmeineke |
1049 |
} |
461 |
mmeineke |
1052 |
|
462 |
|
|
// read and set the frames |
463 |
|
|
|
464 |
mmeineke |
1060 |
openFile(); |
465 |
mmeineke |
1058 |
|
466 |
|
|
fprintf( stdout, |
467 |
|
|
"\n" |
468 |
|
|
"Counting the number of frames in \"%s\"...", |
469 |
|
|
inName ); |
470 |
|
|
fflush(stdout); |
471 |
|
|
|
472 |
mmeineke |
1060 |
setFrames(); |
473 |
mmeineke |
1052 |
|
474 |
mmeineke |
1058 |
fprintf( stdout, |
475 |
|
|
"done.\n" |
476 |
mmeineke |
1060 |
"nFrames = %d.\n", |
477 |
mmeineke |
1058 |
nFrames ); |
478 |
|
|
fflush(stdout); |
479 |
|
|
|
480 |
|
|
if(scdCorr){ |
481 |
|
|
|
482 |
|
|
fprintf ( stdout, |
483 |
|
|
"Calculating the Scd correlation\n" ); |
484 |
|
|
fflush( stdout ); |
485 |
|
|
|
486 |
mmeineke |
1060 |
calcScdCorr( startTime, atoms, outPrefix ); |
487 |
mmeineke |
1058 |
} |
488 |
mmeineke |
1060 |
|
489 |
|
|
if(directorHead){ |
490 |
|
|
|
491 |
|
|
fprintf ( stdout, |
492 |
|
|
"Calculating the Head director\n" ); |
493 |
|
|
fflush( stdout ); |
494 |
|
|
|
495 |
|
|
calcDirHeadCorr( startTime, atoms, outPrefix ); |
496 |
|
|
} |
497 |
mmeineke |
1062 |
|
498 |
|
|
if(directorWhole){ |
499 |
|
|
|
500 |
|
|
fprintf ( stdout, |
501 |
|
|
"Calculating the bilayer director\n" ); |
502 |
|
|
fflush( stdout ); |
503 |
|
|
|
504 |
|
|
calcDirWholeCorr( startTime, atoms, outPrefix ); |
505 |
|
|
} |
506 |
mmeineke |
1073 |
|
507 |
|
|
if(doRMSD){ |
508 |
|
|
|
509 |
|
|
fprintf ( stdout, |
510 |
|
|
"Calculating the RMSD\n" ); |
511 |
|
|
fflush( stdout ); |
512 |
|
|
|
513 |
mmeineke |
1085 |
rmsd( rmsdType, startTime, outPrefix, rmsdName ); |
514 |
mmeineke |
1073 |
} |
515 |
mmeineke |
1080 |
|
516 |
|
|
if(doGofz){ |
517 |
|
|
|
518 |
|
|
fprintf ( stdout, |
519 |
|
|
"Calculating the gofZ\n" ); |
520 |
|
|
fflush( stdout ); |
521 |
|
|
|
522 |
|
|
calcGofz( startTime, atoms, outPrefix ); |
523 |
|
|
} |
524 |
mmeineke |
1085 |
|
525 |
|
|
if(doAvgXY){ |
526 |
|
|
|
527 |
|
|
fprintf ( stdout, |
528 |
|
|
"Calculating the average XY\n" ); |
529 |
|
|
fflush( stdout ); |
530 |
|
|
|
531 |
|
|
avgXY = calcAverageXY( startTime ); |
532 |
|
|
|
533 |
|
|
fprintf ( stdout, |
534 |
|
|
"Done, average XY = %6G\n", avgXY ); |
535 |
|
|
fflush( stdout ); |
536 |
|
|
|
537 |
|
|
} |
538 |
mmeineke |
1058 |
|
539 |
|
|
|
540 |
mmeineke |
1060 |
closeFile(); |
541 |
|
|
|
542 |
mmeineke |
1058 |
} |
543 |
|
|
|
544 |
|
|
|
545 |
|
|
/*************************************************************************** |
546 |
|
|
* prints out the usage for the command line arguments, then exits. |
547 |
|
|
***************************************************************************/ |
548 |
|
|
|
549 |
|
|
void usage(){ |
550 |
|
|
(void)fprintf(stdout, |
551 |
|
|
"\n" |
552 |
|
|
"The proper usage is: %s [options] <input_file>\n" |
553 |
|
|
"\n" |
554 |
|
|
"Options:\n" |
555 |
|
|
"\n" |
556 |
|
|
" short:\n" |
557 |
|
|
" ------\n" |
558 |
|
|
" -o <name> The output prefix\n" |
559 |
|
|
" -t <time> Set the start time for correlations\n" |
560 |
|
|
" -l <maxLength> set the maximum value of r\n" |
561 |
|
|
" *Defaults to 1/2 smallest length of first frame.\n" |
562 |
|
|
" -s Calculate the Scd chain correlation.\n" |
563 |
mmeineke |
1062 |
" -h Calculate the directors for the head groups\n" |
564 |
mmeineke |
1080 |
" -w Calculate the director from the bilayers\n" |
565 |
|
|
" -g Calculate the gofz profile\n" |
566 |
mmeineke |
1058 |
"\n" |
567 |
|
|
" long:\n" |
568 |
|
|
" -----\n" |
569 |
mmeineke |
1073 |
" --rmsd <atom1> rmsd for atom1\n" |
570 |
mmeineke |
1058 |
" --gofrTheta <atom1> <atom2> g(r, theta) for atom1 and atom2\n" |
571 |
|
|
" --gofrOmega <atom1> <atom2> g(r, omega) for atom1 and atom2\n" |
572 |
|
|
" --version displays the version number\n" |
573 |
|
|
" --help displays this help message.\n" |
574 |
|
|
|
575 |
|
|
"\n" |
576 |
|
|
"\n", |
577 |
|
|
programName); |
578 |
|
|
} |